MicroRNA determinants of neuroendocrine differentiation in metastatic castration-resistant prostate cancer

Abstract

Therapy-induced neuroendocrine prostate cancer (NEPC), an extremely aggressive variant of castration-resistant prostate cancer (CRPC), is increasing in incidence with the widespread use of highly potent androgen receptor (AR)-pathway inhibitors (APIs) such as Enzalutamide (ENZ) and Abiraterone and arises via a reversible trans-differentiation process, referred to as neuroendocrine differentiation (NED). The molecular basis of NED is not completely understood leading to a lack of effective molecular markers for its diagnosis. Here, we demonstrate for the first time, that lineage switching to NE states is accompanied by key miRNA alterations including downregulation of miR-106a~363 cluster and upregulation of miR-301a and miR-375. To systematically investigate the key miRNAs alterations driving therapy-induced NED, we performed small RNA-NGS in a retrospective cohort of human metastatic CRPC clinical samples + PDX models with adenocarcinoma features (CRPC-adeno) vs those with neuroendocrine features (CRPC-NE). Further, with the application of machine learning algorithms to sequencing data, we trained a ‘miRNA classifier’ that could robustly classify ‘CRPC-NE’ from ‘CRPC-Adeno’ cases. The performance of classifier was validated in an additional cohort of mCRPC patients and publicly available PCa cohorts. Importantly, we demonstrate that miR-106a~363 cluster pleiotropically regulate cardinal nodal proteins instrumental in driving NEPC including Aurora Kinase A, N-Myc, E2F1 and STAT3. Our study has important clinical implications and transformative potential as our ‘miRNA classifier’ can be used as a molecular tool to stratify mCRPC patients into those with/without NED and guide treatment decisions. Further, we identify novel miRNA NED drivers that can be exploited for NEPC therapeutic targeting.

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Fig. 1: Small RNA sequencing analyses of CRPC-Adeno and CRPC-NE clinical samples, PDX and cellular models.
Fig. 2: A microRNA classifier to distinguish between CRPC-NE and CRPC Adenocarcinoma cases.
Fig. 3: Predominant differential expression of microRNA isoforms (iso-miRs) is associated with neuroendocrine differentiation in CRPC.
Fig. 4: Small RNA sequencing analyses of validation cohort of mCRPC patients.
Fig. 5: Dysregulated miRNAs target signaling pathways implicated in PCa and key genes in ‘NEPC gene signature’ and ‘androgen receptor signaling’.
Fig. 6: Downregulation of miR-106a~363 cluster of miRNAs (including miR-363-3p, miR-20b-5p and miR-106a-5p) drives NEPC via pleiotropic regulation of multiple NEPC drivers.
Fig. 7: miR-363 downregulation is an important alteration in NEPC that directly regulates Aurora Kinase A.
Fig. 8: Upregulation of miR-375 and miR-301a drive neuroendocrine differentiation states in prostate cancer.

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Acknowledgements

We sincerely thank Dr. Paul Jedlicka at University of Colorado, Denver for miR-106a~363 sponge and control constructs and Dr. Felix Feng at UCSF for LNCaP-AR-Enzalutamide resistant cell line. This work is supported by the US Army Medical Research Acquisition Activity (USAMRAA) through the Idea Development Award under Award No. W81XWH-18-1-0303. Additionally, supported by Award no. W81XWH-18-2-0013, W81XWH-18-2-0015, W81XWH-18-2-0016, W81XWH-18-2-0017, W81XWH-18-2-0018, and W81XWH-18-2-0019 Prostate Cancer Biorepository Network (PCBN). Funding support by the National Cancer Institute at the National Institutes of Health (Grant Number RO1CA177984) is also acknowledged. Opinions, interpretations, conclusions, and recommendations are those of the author and are not necessarily endorsed by the Department of Defense or the U.S. Army.

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Bhagirath, D., Liston, M., Patel, N. et al. MicroRNA determinants of neuroendocrine differentiation in metastatic castration-resistant prostate cancer. Oncogene (2020). https://doi.org/10.1038/s41388-020-01493-8

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